I suspect to ulimit and `disk quota. After disabling the disk quota, the problem is still exist. Unfortunately, limits are equal under root and john. Here is the output of ulimit -a (thanks to @Eric DANNIELOU):

" suspect to ulimit and disk quota. After disabling the disk quota, the problem is still exist" : Then try to increase John user limits?
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user130370Dec 24 '12 at 9:59

But what kinds of limitation can be the reason?
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ahmadDec 24 '12 at 14:49

Maximum number of file descriptors for example : ulimit -a as John will give you all possible limitations. Feel free to edit /etc/security/limits.conf accordingly, once you have found.
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user130370Dec 24 '12 at 14:59

Thank! But no luck! root and john have the same limitations (added into the question). Any other idea? :(
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ahmadDec 24 '12 at 15:07

1

strace the R process to see if it hangs somewhere?
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user130370Dec 24 '12 at 15:30

1 Answer
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I'm not sure it will be relevant, but you should really use su - john instead of su john : that way it will invoke a clean login shell. Please check that, doing so, the ulimit -a could now possibly show some relevant differences?

Another thing: use strace -f R instead of strace R so that when it invokes a child process, strace traces that child also and shows exactly where that one hangs.